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- PDB-2wx4: Asymmetric trimer of the Drosophila melanogaster DCP1 C-terminal ... -

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Basic information

Entry
Database: PDB / ID: 2wx4
TitleAsymmetric trimer of the Drosophila melanogaster DCP1 C-terminal domain
ComponentsDECAPPING PROTEIN 1
KeywordsSTRUCTURAL PROTEIN / ASYMMETRIC ASSEMBLY / TRIMERIZATION MODULE / MRNA DECAPPING / P-BODY COMPONENT
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / regulation of cytoplasmic mRNA processing body assembly / pole plasm / pole plasm oskar mRNA localization / deadenylation-independent decapping of nuclear-transcribed mRNA / positive regulation of mRNA catabolic process / deadenylation-dependent decapping of nuclear-transcribed mRNA / miRNA-mediated post-transcriptional gene silencing / P granule / nuclear-transcribed mRNA catabolic process ...mRNA decay by 5' to 3' exoribonuclease / regulation of cytoplasmic mRNA processing body assembly / pole plasm / pole plasm oskar mRNA localization / deadenylation-independent decapping of nuclear-transcribed mRNA / positive regulation of mRNA catabolic process / deadenylation-dependent decapping of nuclear-transcribed mRNA / miRNA-mediated post-transcriptional gene silencing / P granule / nuclear-transcribed mRNA catabolic process / enzyme activator activity / P-body / mRNA processing / mRNA binding / identical protein binding / cytoplasm
Similarity search - Function
Helix Hairpins - #2030 / mRNA-decapping enzyme, C-terminal / mRNA-decapping enzyme C-terminus / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / Helix Hairpins / Helix non-globular / Special / PH-like domain superfamily
Similarity search - Domain/homology
Decapping protein 1, isoform A
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTritschler, F. / Weichenrieder, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Dcp1 Forms Asymmetric Trimers to Assemble Into Active Mrna Decapping Complexes in Metazoa.
Authors: Tritschler, F. / Braun, J.E. / Motz, C. / Igreja, C. / Haas, G. / Truffault, V. / Izaurralde, E. / Weichenrieder, O.
History
DepositionNov 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DECAPPING PROTEIN 1
B: DECAPPING PROTEIN 1
C: DECAPPING PROTEIN 1
D: DECAPPING PROTEIN 1
E: DECAPPING PROTEIN 1
F: DECAPPING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,77611
Polymers31,2966
Non-polymers4805
Water97354
1
A: DECAPPING PROTEIN 1
B: DECAPPING PROTEIN 1
C: DECAPPING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8405
Polymers15,6483
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-74.58 kcal/mol
Surface area7430 Å2
MethodPISA
2
D: DECAPPING PROTEIN 1
E: DECAPPING PROTEIN 1
F: DECAPPING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9366
Polymers15,6483
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-99.73 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.920, 120.920, 134.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein/peptide
DECAPPING PROTEIN 1 / DCP1


Mass: 5215.934 Da / Num. of mol.: 6 / Fragment: TRIMERIZATION DOMAIN, RESIDUES 328-366
Source method: isolated from a genetically manipulated source
Details: EC6.1.1.- IN UNIPROT DISPUTED BY AUTHOR / Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q9W1H5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL CLONING TAG - GPHMADL

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 73 % / Description: NONE
Crystal growpH: 6.5
Details: 100 MM MES (PH6.5), 1.2 M AMMONIUM SULFATE, 5% 1,4-DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0643
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 12, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111)MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0643 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 14564 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 55.2 Å2 / Rsym value: 0.11 / Net I/σ(I): 13
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.8 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WX3 TRUNCATED POLY-ALA MODEL

2wx3


Resolution: 2.8→48.79 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.879 / SU B: 10.537 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES A359-A366,B321-B325,C364-C366,D366,E321-E322,E366,F321 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.26675 730 5 %RANDOM
Rwork0.21482 ---
obs0.21725 13830 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å2-0 Å2
2--0.16 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 25 54 2132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222112
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9612855
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0225249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.95826.204108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.3415363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021572
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7821.51267
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53122014
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8623845
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2234.5841
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 53 -
Rwork0.283 972 -
obs--96.15 %

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